Point 1: Do you intend to have both powered at the same time? That might make a difference. Which leads me right into point #2
Point 2: If you have them both powered, that might cause problems. The cthulhu board is USB based, no? Then it runs off of +5v give or take half a volt. The PS2 controllers operate somewhere between 5v-3.3v for the VCC and 9v-7.9v for the motor (depending on what reference source you use). I don't know how either controller will respond to a voltage disparity but I would guess the USB fuses would trip if they go above a certain voltage. Heck, I don't even know if the controller will send that kind of voltage up the USB lines if it gets that voltage from the other side.
Point 3: I haven't taken apart a PS2 controller so I'm just going on a possible caveat emptor on other controllers. Depending on how the PS2 circuit is laid out, it's possible that the buttons aren't true +5v->0v kind of thing arcades typically use. For example, one PC controller I tore apart had no way to tap directly into the IC (like I wanted) since, as near as I can figure, some of the buttons were a +5v->0v arrangement, while two appeared to be a pulsed AC signal (with diodes naturally) so when the IC pulled the signal up to +5v on button A, it would see if it was pulled to 0. Then it would flip the polarity for button B and see if that was pulled down to 0v. And still haven't quite worked out how two other buttons functioned. Point being, if the controller is doing some weird ---steaming pile of meadow muffin--- with its buttons, you're going to get weird ---steaming pile of meadow muffin--- if you try to cross wire them with another controller. You can get an idea of what's going on if you trace each button back to the IC and make sure there's a 1-1 relationship for each pin (less ground pin). If there is, it's worth a shot. If there's not (like two buttons to one pin) then you can try but don't expect anything. From a discussion I read about the 360 controllers, they like to do weird ---steaming pile of meadow muffin--- with their buttons. But I could be wrong about that, I never took one of those apart either.
I say... try your original idea and see if it works. Make sure you can pull the wiring and retry a different scheme though. IOW, attach really really long leads to the PS2 pads then hot glue the suckers down that way you're not stuck unsoldering/resoldering five or six times. I would start by following the tutorials on hacking PS2 pads to arcade controllers. Then test the set up without the Cthulu board. That way you know it at least that setup works and you're not left trying to figure out what's wrong and looking in the wrong places.
If your idea fails, just rewire to a new idea.